Hi.
On Wed, Sep 2, 2009 at 8:56 PM, Max Moldovan wrote:
>
> Thanks for your information Henrik.
>
> 1. I can extract sigma estimates using you first suggestion:
>
> rawCNs <- extractRawCopyNumbers(cbs, array=3, chromosome=9);
> sigma <- estimateStandardDeviation(rawCNs);
>
> A colleague of mine r
Thanks for your information Henrik.
1. I can extract sigma estimates using you first suggestion:
rawCNs <- extractRawCopyNumbers(cbs, array=3, chromosome=9);
sigma <- estimateStandardDeviation(rawCNs);
A colleague of mine recommended an alternative way apparently leading
to the same results (in
Hi.
On Wed, Sep 2, 2009 at 11:26 AM, Diya Vaka wrote:
> Hi,
>
> I have created a cdf and I am trying to check how its running and I have
> have this error.Could anyone help me on this.
>
> This is the code:
>>
>> df<-GenericDataFile("annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2.cdf")
>>
Hi.
On Tue, Sep 1, 2009 at 10:04 PM, Max Moldovan wrote:
>
> Hi People,
>
> I have the following sequence of commands:
>
> chipType <- "GenomeWideSNP_5";
> cdfTags <- "Full,r2";
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags=cdfTags)
> print(cdf)
> gi <- getGenomeInformation(cdf)
> print(gi
Hi Mark
Thanks for this - very helpful - I was thinking about it in the wrong
way.
Just for the benefit of this thread, something that I should have
realised, if you type
?MatSmoothing
you can see the description of probeWindow relative to BandWidth, and
the other arguments that this function tak
Hi Sabrina.
Hmm, that does seem unexpected. I would expect that if there are just
a few probes picked out, it shouldn't change that much.
Can you give more details about this new CDF you made? Would it be
similar to the existing 'core' CDF? Presumably, there will be a large
overlap with
Hi, all
I am working on mouse Exon arrays from Affy. Because there are probes
with multiple hits on the genome, I screened out these probes and
exons with only one probe and transcript clusters with one exon on the
array. After that I created a CDF file as illustrated from this group.
My problems
Hi,
I have created a cdf and I am trying to check how its running and I have
have this error.Could anyone help me on this.
This is the code:
>
df<-GenericDataFile("annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2.cdf")
> chipType<-"HG-U133_Plus_2"
> cdf<-AffymetrixCdfFile$findByChipType(chi
On Wed, Sep 2, 2009 at 8:28 AM, JeromeW wrote:
>
> Thank you Henrik for your quick reply.
>
> Here is what I get:
>
>> df <-
>> GenericDataFile("annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf");
>> df;
> GenericDataFile:
> Name: GenomeWideSNP_6
> Tags: Full
> Full name: GenomeW
Thank you Henrik for your quick reply.
Here is what I get:
> df <-
> GenericDataFile("annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf");
> df;
GenericDataFile:
Name: GenomeWideSNP_6
Tags: Full
Full name: GenomeWideSNP_6,Full
Pathname: annotationData/chipTypes/GenomeWideSNP_6/
So, if none of the stopifnot() tests complaints, then it might be that
the CDF file might be corrupt or incomplete. Compare with the file
size and checksum that I get:
> library("aroma.affymetrix");
> pathname <-
> "annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.cdf";
> df <- Gen
No worries at all - I just want you and everyone else to know how to
make this forum more effective, which is somewhat explained in that
FAQ. 2008-03-26:
http://groups.google.com/group/aroma-affymetrix/web/frequently-asked-questions
Cheers,
Henrik
On Tue, Sep 1, 2009 at 11:58 AM, ssv wrote
(sorry for quoting myself)>
I am more and more puzzled... The "findByChipType" method seems to
correctly detect the cdf file:
AffymetrixCdfFile$findByChipType("GenomeWideSNP_6", tags="Full")
[1] "annotationData/chipTypes/GenomeWideSNP_6/
GenomeWideSNP_6,Full.cdf"
--~--~-~--~~-
Hi all
I reply in this thread because I also have the "could not locate a
file" problem which I cannot solve.
My code:
setwd("/x05/people/m140932/eclipse/workspace/CNV"); # here I set the
working directory
library("aroma.affymetrix");
log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
o
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